Freie Universität Berlin
Fachbereich Mathematik und Informatik
German Research Foundation (DFG)
Spatiotemporal Simulation of Module Assembly and Function
Our project deals with the spatiotemporal simulation of assembly and function of modules. We are continuing to develop efficient computational methods for the specific simulation requirements of such systems. Our main focus is on modeling rod phototransduction, initiated by Rhodopsin activation through light (with D1).
We will compute Rhodopsin dimer affinities depending on the conformational state (R/R*) using adaptive molecular dynamics simulation, and use these results in order to simulate the assembly of supramolecular Rhodopsin structures with our software package ReaDDy. In parallel, we will continue to study Dynamin oligomerization and dynamics (with C7). Here, we will probe particular domain interactions (G-G, Stalk-Stalk, Stalk-G) using adaptive molecular dynamics, and then simulate the assembly of oligomers. By investigating the assembly and function of two modular systems we hope to work out overarching principles that go beyond specific mechanisms of an individual protein system.